Week 10

Question 1

3 types of RNA

Answer 1

T, M, R

Question 2

Transcription steps (3)

Answer 2

1. rna polymerase recruited at promoter with help of sigma factor
2. rna polymerase synthesizes rna as bubble of unwound dna moves along
3. at termination site both rna and rna polymerase are released, secondary structure, enzyme mediated

Question 3

Proteins general functions (3)

Answer 3

catalytic proteins (enzymes)
structural proteins (parts of membranes, cell envelope, ribosomes)
regulatory proteins (dna binding, affecting transcription)

Question 4

Primary structure

Answer 4

linear array of amino acids in a polypeptide, folds to form a more stable structure

Question 5

protein composition

Answer 5

polymers of amino acids, both amino, carboxylic acid, linked to a-carbon

Question 6

how are amino acids linked?

Answer 6

by polypeptide bonds through carboxyl carbon of one amino acid and amino nitrogen of a second

Question 7

polypeptide

Answer 7

many amino acid links, proteins consist of 1+ polypeptides

Question 8

amino acids, secondary structure

Answer 8

form hydrogen bonding (alpha helix or beta sheet)

Question 9

amino acids, tertiary structure

Answer 9

three dimensional shape of a polypeptide from hydrophobic and other interactions

Question 10

quaternary structure, amino acids

Answer 10

number and types of polypeptides that make a protein

Question 11

denaturation

Answer 11

loss of structure and biological properties

Question 12

transfer rnas

Answer 12

carry amino acids to translation machinery

Question 13

anticodon

Answer 13

three bases that recognize codon (3 nucleic acids encoding an amino acid)

trna cognate (correct) amino acid brought together by aminoacyl-trna synthetases

Question 14

general structure of trnas

Answer 14

single stranded
extensive secondary structure
contain bases modified post transcription
extensive double stranded regions formed by internal base pairing
cloverleaf shape
3’ end always had CCA added by CCA-adding enzyme instead of being encoded

Question 15

Genetic code

Answer 15

a triplet of nucleic acid bases (codon) encoded a specific amino acid
64 possible codons
specific codons for starting and stopping translation

Question 16

Degenerate code

Answer 16

multiple codons encode a singular amino acid (64 codons versus 22 natural amino acids) lacks one to one correspondence

Question 17

Codon recognition occurs by:

Answer 17

specific base pairing with complementary anticodon sequence on trna
some trnas recog 1+

Question 18

wobble

Answer 18

irregular base pairing allowed at third position of trna

Question 19

codon bias

Answer 19

multiple codons for the same amino acid are not used equally
varies between organisms
correlated with trna concentration

Question 20

start codon

Answer 20

translation begins with aug encoded n-formylmethionine in bacteria and methionine in archaea and eukarya

Question 21

reading frame

Answer 21

triplet code required translation to begin at the correct nucleotide

RBS ensures proper reading frame in bacteria

Question 22

stop (nonsense) codons

Answer 22

terminate translation (uaa, uag, uga) sometimes unusual amino acids selenocysteine and pyrrolysine can be encoded by stop codons

Question 23

open reading frame

Answer 23

AUG followed by a number of codons and a stop codon

Question 24

mechanisms of protein synthesis

Answer 24

3 steps, initiation, elongation, termination
mrna, trna, ribosomes
multiple proteins
needs GTP for energy

Question 25

ribosomes

Answer 25

large complexes of proteins and rna where proteins are biosynthesized

Question 26

polysomes

Answer 26

a complex formed by multiple ribosomes simultaneously translating a single mrna

Question 27

release factors

Answer 27

recognize stop codon and cleave polypeptide from trna

Question 28

dna binding proteins

Answer 28

bind to specific sites
different mechanisms

Question 29

negative regulation, repression

Answer 29

inhibits gene expression, response to overabundance of an end product, mediated by repressor proteins. typically affects anabolic enzymes

Question 30

negative regulation, induction

Answer 30

production of an enzyme in response to a signal or inducer, alleviates binding of repressor that blocks transcription, typically affects catabolic enzymes

Question 31

positive regulation

Answer 31

activator binds to regulatory protein, directly activates transcription, binding sites on dna, improves recruitment and binding of rna pol to weak promoter

Question 32

two component systems

Answer 32

prokaryotes regularly cellular metabolism in response to environmental fluctuations
1. ext signal transmitted directly to the target
2. ext signal detected by a sensor and then transmitted to regulatory machinery

Question 33

sensor kinase

Answer 33

in cytoplasmic membrane, detects environmental signal and autophosphorylates

Question 34

response regulator

Answer 34

in cytoplasm, dna binding protein that regulates transcription, also has feedback loop, terminates signal

Question 35

quorum sensing

Answer 35

mechanism by which bacteria assess their population density
ensures sufficient # of cells present before initiating a response
autoinducers act as messengers to sense cell density

Question 36

autoinducers

Answer 36

species specific molecules
diffuse freely across cell envelope
reach high concen inside cells only if many cells near
bone to specific activator proteins and trigger transcription of specific genes

Question 37

chemotaxis

Answer 37

bacteria and archaea respond to challenges such as nutrient limitation and toxin accumulation by moving towards attractants and away from repellants